Refining intra-protein contact prediction by graph analysis.

ABSTRACT:

Background

Accurate prediction of intra-protein residue contacts from sequence information will allow the prediction of protein structures. Basic predictions of such specific contacts can be further refined by jointly analyzing predicted contacts, and by adding information on the relative positions of contacts in the protein primary sequence.

Results

We introduce a method for graph analysis refinement of intra-protein contacts, termed GARP. Our previously presented intra-contact prediction method by means of pair-to-pair substitution matrix (P2PConPred) was used to test the GARP method. In our approach, the top contact predictions obtained by a basic prediction method were used as edges to create a weighted graph. The edges were scored by a mutual clustering coefficient that

SUBMITTER: Frenkel-Morgenstern M 

PROVIDER: S-EPMC1892094 | biostudies-literature | 2007 May

REPOSITORIES: biostudies-literature